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Crystal Structure of Human APRT wild type in complex with GMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6FCH
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 NaOAc, PEG4000, Glycerol, Tris
Crystal Properties Matthews coefficient Solvent content 2.28 45.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.38 α = 76.73 b = 47.68 β = 69.27 c = 47.79 γ = 61.48
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2014-10-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 1 0.9786 SOLEIL PROXIMA 1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.55 44.57 94.6 0.046 0.046 0.059 0.036 0.997 9.1 2.3 47120
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.55 1.63 93.1 0.303 0.31 0.23 0.619 2.3 2.2 6818
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 6FCH 1.55 44.57 44806 2314 94.64 0.1584 0.1575 0.1702 0.177 0.1869 RANDOM 23.571
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.03 0.48 -0.22 -0.04 0.04 0.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.958 r_dihedral_angle_4_deg 22.138 r_dihedral_angle_3_deg 12.361 r_dihedral_angle_1_deg 5.774 r_mcangle_it 2.647 r_mcbond_it 1.929 r_mcbond_other 1.912 r_angle_refined_deg 1.098 r_angle_other_deg 0.568 r_chiral_restr 0.066
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.958 r_dihedral_angle_4_deg 22.138 r_dihedral_angle_3_deg 12.361 r_dihedral_angle_1_deg 5.774 r_mcangle_it 2.647 r_mcbond_it 1.929 r_mcbond_other 1.912 r_angle_refined_deg 1.098 r_angle_other_deg 0.568 r_chiral_restr 0.066 r_bond_refined_d 0.007 r_gen_planes_refined 0.006 r_bond_other_d r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2676 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 48
Software Software Software Name Purpose REFMAC refinement SCALA data scaling PHASER phasing PDB_EXTRACT data extraction Coot model building MxCuBE data collection iMOSFLM data reduction